LOCUS       NM_001107837            3421 bp    mRNA    linear   ROD 23-MAR-2023
DEFINITION  Rattus norvegicus LIM homeobox 6 (Lhx6), mRNA.
ACCESSION   NM_001107837 XM_001079382 XM_231175
VERSION     NM_001107837.2
KEYWORDS    RefSeq; RefSeq Select.
SOURCE      Rattus norvegicus (Norway rat)
  ORGANISM  Rattus norvegicus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
            Muroidea; Muridae; Murinae; Rattus.
REFERENCE   1  (bases 1 to 3421)
  AUTHORS   Oh SG, Hwang YG and Lee HS.
  TITLE     LIM homeobox 6 (Lhx6)+ neurons in the ventral zona incerta project
            to the core portion of the lateral supramammillary nucleus in the
            rat
  JOURNAL   Brain Res 1748, 147125 (2020)
   PUBMED   32931819
  REMARK    GeneRIF: LIM homeobox 6 (Lhx6)+ neurons in the ventral zona incerta
            project to the core portion of the lateral supramammillary nucleus
            in the rat.
REFERENCE   2  (bases 1 to 3421)
  AUTHORS   Jeong MS, Hwang EY, Kim HT, Yoo MA and Jang SB.
  TITLE     Purification of caudal-related homeodomain transcription factor and
            its binding characterization
  JOURNAL   J Microbiol Biotechnol 19 (12), 1557-1564 (2009)
   PUBMED   20075618
  REMARK    GeneRIF: Studied the DNA binding activity of human CDX2. Three
            CDX2-binding proteins were found in rat gastric tissue, and those
            proteins were identified to the homeobox protein Hox-D8, LIM
            homeobox protein 6, and SMC1L1 protein.
REFERENCE   3  (bases 1 to 3421)
  AUTHORS   Du T, Xu Q, Ocbina PJ and Anderson SA.
  TITLE     NKX2.1 specifies cortical interneuron fate by activating Lhx6
  JOURNAL   Development 135 (8), 1559-1567 (2008)
   PUBMED   18339674
REFERENCE   4  (bases 1 to 3421)
  AUTHORS   Liodis P, Denaxa M, Grigoriou M, Akufo-Addo C, Yanagawa Y and
            Pachnis V.
  TITLE     Lhx6 activity is required for the normal migration and
            specification of cortical interneuron subtypes
  JOURNAL   J Neurosci 27 (12), 3078-3089 (2007)
   PUBMED   17376969
REFERENCE   5  (bases 1 to 3421)
  AUTHORS   Mori T, Yuxing Z, Takaki H, Takeuchi M, Iseki K, Hagino S, Kitanaka
            J, Takemura M, Misawa H, Ikawa M, Okabe M and Wanaka A.
  TITLE     The LIM homeobox gene, L3/Lhx8, is necessary for proper development
            of basal forebrain cholinergic neurons
  JOURNAL   Eur J Neurosci 19 (12), 3129-3141 (2004)
   PUBMED   15217369
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            JACYVU010000115.1.
            
            On Dec 7, 2020 this sequence version replaced NM_001107837.1.
            
            ##Evidence-Data-START##
            RNAseq introns :: single sample supports all introns SAMN11044071
                              [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            inferred exon combination :: based on alignments, homology
            RefSeq Select criteria    :: based on conservation, expression,
                                         longest protein
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-147               JACYVU010000115.1  12912692-12912838   c
            148-219             JACYVU010000115.1  12911451-12911522   c
            220-402             JACYVU010000115.1  12910888-12911070   c
            403-524             JACYVU010000115.1  12910400-12910521   c
            525-745             JACYVU010000115.1  12901837-12902057   c
            746-846             JACYVU010000115.1  12899204-12899304   c
            847-942             JACYVU010000115.1  12898918-12899013   c
            943-1117            JACYVU010000115.1  12898560-12898734   c
            1118-1221           JACYVU010000115.1  12894777-12894880   c
            1222-3421           JACYVU010000115.1  12889285-12891484   c
FEATURES             Location/Qualifiers
     source          1..3421
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /strain="BN"
                     /db_xref="taxon:10116"
                     /chromosome="3"
                     /map="3p11"
     gene            1..3421
                     /gene="Lhx6"
                     /note="LIM homeobox 6"
                     /db_xref="GeneID:311901"
                     /db_xref="RGD:1306174"
     exon            1..147
                     /gene="Lhx6"
                     /inference="alignment:Splign:2.1.0"
     CDS             64..1242
                     /gene="Lhx6"
                     /note="LIM homeobox protein 6"
                     /codon_start=1
                     /product="LIM/homeobox protein Lhx6"
                     /protein_id="NP_001101307.2"
                     /db_xref="GeneID:311901"
                     /db_xref="RGD:1306174"
                     /translation="

MYWKHESAAPALPEGCRLPAEGGPTTDQVMAQPGSGCKATTRCLEGTAPPAMAQSDAEALAGALDKDEGRASPCTPSTPSVCSPPSAASSVPSAGKNICSSCGLEILDRYLLKVNNLIWHVRCLECSVCRTSLRQQNSCYIKNKEIYCKMDYFSRFGTKCARCGRQIYASDWVRRARGNAYHLACFACFSCKRQLSTGEEFGLVEEKVLCRIHYDTMIENLKRAAENGNGLTLEGAVPSEQDSQPKPAKRARTSFTAEQLQVMQAQFAQDNNPDAQTLQKLADMTGLSRRVIQVWFQNCRARHKKHTPQHPVPPSGAPPSRLPSSLSDDIHYSPFSSPERARMVTLHGYIESQVQCGQVHCRLPYTAPPVHLKADMDGPLSSRGEKVILFQY"

     misc_feature    358..519
                     /gene="Lhx6"
                     /note="The first LIM domain of Lhx6; Region: LIM1_Lhx6;
                     cd09380"
                     /db_xref="CDD:188766"
     misc_feature    order(358..360,367..369,421..423,430..432,439..441,
                     448..450,505..507,514..516)
                     /gene="Lhx6"
                     /note="Zn binding site [ion binding]; other site"
                     /db_xref="CDD:188766"
     misc_feature    541..705
                     /gene="Lhx6"
                     /note="The second LIM domain of Lhx6; Region: LIM2_Lhx6;
                     cd09382"
                     /db_xref="CDD:188768"
     misc_feature    order(541..543,550..552,607..609,616..618,625..627,
                     634..636,691..693,700..702)
                     /gene="Lhx6"
                     /note="Zn binding site [ion binding]; other site"
                     /db_xref="CDD:188768"
     misc_feature    order(808..822,826..828,877..879,895..897,934..936,
                     940..945,952..957,961..969,973..978)
                     /gene="Lhx6"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    order(814..816,823..825,943..945,952..957,964..966)
                     /gene="Lhx6"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     misc_feature    817..975
                     /gene="Lhx6"
                     /note="Homeobox domain; Region: Homeobox; pfam00046"
                     /db_xref="CDD:425441"
     exon            148..219
                     /gene="Lhx6"
                     /inference="alignment:Splign:2.1.0"
     exon            220..402
                     /gene="Lhx6"
                     /inference="alignment:Splign:2.1.0"
     exon            403..524
                     /gene="Lhx6"
                     /inference="alignment:Splign:2.1.0"
     exon            525..745
                     /gene="Lhx6"
                     /inference="alignment:Splign:2.1.0"
     exon            746..846
                     /gene="Lhx6"
                     /inference="alignment:Splign:2.1.0"
     exon            847..942
                     /gene="Lhx6"
                     /inference="alignment:Splign:2.1.0"
     exon            943..1117
                     /gene="Lhx6"
                     /inference="alignment:Splign:2.1.0"
     exon            1118..1221
                     /gene="Lhx6"
                     /inference="alignment:Splign:2.1.0"
     exon            1222..3421
                     /gene="Lhx6"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

cgaggccccactccgtgctgctctttgcgctgcgcgcccttcgagccctcagttcccgggcccatgtactggaagcatgagagcgccgccccggcgctgcccgagggctgccggttaccggcggagggcggccccaccaccgaccaggtgatggcccagccagggtccggctgcaaagcgaccacccgctgtcttgaagggaccgctccgcctgccatggctcagtcagacgccgaggccttggcaggcgctctggacaaggacgaaggtagagcctccccatgtacgcccagcacaccctctgtctgctcgccgccctctgccgcctcttccgtgccgtctgctggcaagaatatctgctccagttgcggtctcgagatcctggaccggtatctgctcaaggtcaacaacctcatctggcacgtgcggtgcctcgagtgctccgtgtgtcgcacatcgctgaggcagcagaatagctgctacatcaagaacaaggagatctactgcaagatggactacttcagccgatttggaaccaagtgtgcccggtgcggcagacaaatctatgccagtgactgggtgcggcgcgcgcgcggcaatgcctaccacctggcctgcttcgcttgcttttcctgcaagcgccagctatccacgggcgaggaattcggcctggttgaggagaaggtgctttgccgcatccattacgacaccatgatcgagaacctcaagagggccgccgagaacgggaacggtctcacgttggagggggcagtgccctcggaacaggacagtcagcccaagccagctaagcgcgcgcggacgtccttcacggcagagcaattgcaggttatgcaggctcagttcgcgcaggacaacaaccccgacgcgcagacgctgcagaagctagcggacatgacgggcctcagtcgcagggtcatccaggtgtggtttcaaaactgccgagcgcgtcataaaaagcatacaccgcagcacccagtgccgccctctggggcacccccgtcccgcctcccctcctccctgtccgacgacatccactattctccgttcagcagcccagagcgggcacgcatggtcaccttgcacggctacatcgagagtcaggtacagtgcgggcaggtgcactgccgactgccttacaccgcgccccctgtccacctcaaagccgacatggatgggccgctctccagccggggtgagaaggtcatcctttttcagtactaactctgccggcgcttgcacatctgtccatgggcaccacacagctgcccctcagccgctgagcatccagcgtccagctgtggccagggatccaccgcctctgggcacaccctcctcacccgctgccgccctgccctctgccagtggccccatcaacccagccccggtatttccctctcctgctgagaaccagaacccgccaggagcagcagagccctctctgggaaggcaggctccctgaaatgtggtatcagcatgaaaacaagcagcctgtctttcctcatcatctgggagtcttgcttatctgggagtcagctgatcgcagcagcaacagctaattcaacaacagcctcccacttcacaggttttcttcttcccccatattggccttcatttactacttccttggaaccgtctctgagttctgaacagccaaaacaacccccaacattatatactccgctgcttttgtctggaaaactctacagtgtttgtgggatgtccccaaaggaaagccgtgttctgattttatcatttccatctgtctggttatgtcaagttaactcagaaaaagaagagacactgaccaaccctgagaggcccaacagggcagagatggaggcctgcccagatgaagaggcagagggatgggcagggatgggtgccaaagaccccccattggcttggagaaggaggactgggtatgctggacttggagaggtgatgagagtttcatggagagaaaagaggaaacttgagggggggtgtcccccacctaattacccagcaggagttgtggaaagaatggcgtctgatcggcacgatgacaccactgaatgtttaggtgggctagcattagggacccttgttggccacttttcagtcctgagatgagggcctgagccagtcttctctgggggtggggtgagactactcatgaggaccaaggaacagagcccagagaaatagcagccatgatattagctcggattcatccacgaggggagagaggtgcccgtggcctcagtgagtgcgtgccaagcccaggattccagctggcacctcggcagtctccccaccaactgcacagagccagctctacccactcctgagagcagaggccagctccaaataaaggtctcaggttacacaggccctcgattcatgttttcagggggtgcccatctgccccgagcttatcctgtaattctacaaccacttggtggcctgatgcactactcaccagaggctgcctagcagcgtgtgttagccaaagtcttcctccctgttttgaggagactccaggtcaggaaaggcaaattccgagtctgtatgctgtccctccttcacctgtggcagacatcactaatcgctaatcgatcacacctctctctctctctctctctctctctctctctctctctctctctgtctctcgctctcgctctcgctctcgctctcgctctctctcgctttctctcgctctcggagtctggataaggtttcagaattcccaagcttgaagttgggatgtgaccaactgtgctattgctgaaggacctggaggagggttaggcctgggtgaccccccagaagggaacttgcatcttttcccttccaaaaattgtcaactgacggaggacagagagaaagttcctcccagaaagctgagagtgtggttcattccggtcagaactccagcaccctgtgccaggcactgactcaagcaagaggaacctggcctgatccctgacttggggaacccagatattccctttgatttattttgctcctaaggatcaaaacccccagttgcaaccatgtggcaagtggccagctgagcccaggttacttggtacccactctgccttgagccttcccccagggtctatttcttgtgtggatcacgtggcagtagcatgttgcagttcagacgtctccactactctgttcaaaacagcctgggaatgtacaggccattgaggctatttatttaaatacacacacacacacacacacacacacacacacacatgcgcacacacaaaggggggaacacacacaaatggaaacaattgtaagcacttttttttgtaaaaccaatgtctgttttgttacatacctttcatgttgtgctttgtaaatgtcttatttgtgtaataaataaagttaatgcgagtag

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